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Recoding the SARS-CoV-2 genome - A multidisciplinary approach to generate live-attenuated coronavirus vaccines

English title Recoding the SARS-CoV-2 genome - A multidisciplinary approach to generate live-attenuated coronavirus vaccines
Applicant Thiel Volker
Number 198473
Funding scheme NRP 78 Covid-19
Research institution Institut für Virologie und Immunologie Depart. Infektionskrankheiten und Pathologie Universität Bern
Institution of higher education Institute of Virology and Immunology - IVI
Main discipline Biochemistry
Start/End 01.11.2020 - 31.10.2022
Approved amount 1'189'457.00
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All Disciplines (3)

Discipline
Biochemistry
Experimental Microbiology
Embryology, Developmental Biology

Keywords (7)

Ribosome profiling; SARS-CoV-2 animal models; Translation; live-attenuated vaccine; Virus attenuation; RNA modification; SARS-CoV-2

Lay Summary (German)

Lead
SARS-CoV-2 löst Entzündungen der oberen Atemwege und der Lunge aus, die das Leben vieler Menschen weltweit bedrohen. Dazu muss das Virus den Zellstoffwechsel umprogrammieren. Um SARS-CoV-2 einzudämmen, wollen wir herausfinden, wo die Schwachstellen des Virus bei der Übernahme der Wirtszelle liegen.
Lay summary

Hintergrund

Wie alle Viren übernimmt SARS-CoV-2 bei der Infizierung die Kontrolle der Translationsprozesse der Wirtszelle. Wir müssen daher die Kernmechanismen kennen, mit denen es die zelluläre Translation umprogrammiert. So können wir das SARS-CoV-2-Genom umkodieren, um abgeschwächte Viren für Impfstoffe zu produzieren. Unter Einsatz etablierter Rekodierungsstrategien zur Virulenzminderung werden diese Viren in Zellkulturen und hochentwickelten Tiermodellen bezüglich verschiedener Aspekte von COVID-19 beurteilt.

Forschungsziele

Um attenuierte SARS-CoV-2 Impfstoffstämme zu produzieren, erforschen wir die RNA-Modifikation durch SARS-CoV-2 und charakterisieren die Translation sowie die Zell-tRNA und ihre Modifikation bei der Infizierung. Nebst der Entwicklung geeigneter umkodierter SARS-CoV-2-Viren schliesst dies eine Beurteilung der Attenuierung, der Sicherheit und der Immunogenität in mehreren Tiermodellen ein.

Erwartete Ergebnisse und Produkte

Unser Projekt beruht auf wiederholter Optimierung. Basierend auf der RNA-Modifikation und -Translation im Rahmen der molekularen Virus-Wirt-Interaktionen entwickeln wir zunächst Impfstoffstämme. Dann prüfen wir deren Attenuierung, Pathogenität und Immunogenität. Schliesslich optimieren wir die aus rekodiertem SARS-CoV-2-Material gewonnenen Impfstoffe durch gezielte Anpassung, um eine Immunschutzreaktion zu erzielen. Die Zielprodukte sind gut charakterisierte SARS-CoV-2-Impfstoffkandidaten, die gezielt designt und in vivo bezüglich Attenuierung, Sicherheit und Immunogenität geprüft werden.

Beitrag zur Bewältigung der aktuellen Pandemie

Unser Projekt ist ein Beitrag zur weltweiten Entwicklung von SARS-CoV-2-Impfstoffen. Die ersten RNA-, Subunit- und vektorbasierten Impfstoffe dürften bald verfügbar sein. Erwartungsgemäss werden sich, sobald weitere Daten zur Wirksamkeit und Sicherheit vorliegen, die Grenzen dieser ersten Generation zeigen. Um diese zu überwinden, müssen SARS-CoV-2-Impfstoffe der zweiten Generation entwickelt und produziert werden, die sich u. a. kostengünstig und einfach herstellen und lagern lassen.

Direct link to Lay Summary Last update: 23.12.2020

Lay Summary (French)

Lead
Le SARS-CoV-2 cause des maladies des voies respiratoires supérieures ainsi que des pneumopathies et met en danger d’innombrables vies dans le monde entier. Pour infecter les cellules, le virus a besoin de reprogrammer leur métabolisme. Notre but est d’identifier les vulnérabilités du virus au cours de son usurpation de la cellule hôte et d’utiliser ces connaissances pour atténuer le SARS-CoV-2.
Lay summary

Contexte

Comme tous les virus, le SARS-CoV-2 a besoin de détourner à son profit la machinerie traductionnelle de la cellule hôte pour réussir à infecter celle-ci. Il est par conséquent important d’identifier les mécanismes essentiels que le virus utilise pour modifier et reprogrammer la traduction cellulaire. Sur la base de ces connaissances, nous pourrons recoder le génome du SARS-CoV-2 et obtenir un virus atténué pour le développement de vaccins. En combinant cette approche avec des stratégies de recodage reconnues pour l’atténuation des virus, nous évaluerons les virus atténués dans des cultures cellulaires et des modèles animaux avancés pour étudier différents aspects du COVID-19.

Objectifs de recherche

Nous étudierons les modifications de l’ARN du SARS-CoV-2 et caractériserons le paysage traductionnel et les niveaux d’ARNt cellulaire ainsi que les modifications de l’ARNt au cours de l’infection, afin de produire des souches de vaccins vivants atténués anti-SARS-CoV-2. Il faudra pour cela produire un SARS-CoV-2 recodé rationnellement et évaluer son atténuation, son innocuité et son immunogénicité dans plusieurs modèles animaux.

Résultats et produits envisagés

Notre projet se base sur un processus d’optimisation itératif. Pour commencer, nous produirons des souches de vaccins conditionnées par des interactions moléculaires virus-hôte dans le contexte de la modification et de la traduction de l’ARN. Dans un second temps, nous évaluerons l’atténuation, le pouvoir pathogène et l’immunogénicité de la souche vaccinale. Enfin, nous affinerons les souches vaccinales de SARS-CoV-2 recodées pour optimiser l’atténuation du virus afin d’induire une réponse immunitaire protectrice. Les produits envisagés sont des candidats vaccins anti-SARS-CoV-2 bien caractérisés, conçus rationnellement et dont l’atténuation, l’innocuité et l’immunogénicité seront évaluées in vivo.

Contribution à la lutte contre la pandémie actuelle

Notre projet se veut une contribution à l’effort mondial de production de vaccins contre le SARS-CoV-2. Nous pensons que la première génération de vaccins à ARN, à sous-unités et à vecteur viral sera rapidement disponible, mais nous pensons aussi que ses limites pourraient apparaître lorsque davantage de données d’efficacité et d’innocuité seront disponibles. Nous prévoyons qu’il restera nécessaire de développer et de produire des vaccins de deuxième génération contre le SARS-CoV-2 qui n’auront pas les défauts éventuels de la première génération et seront notamment plus faciles à produire et à stocker et d’un meilleur rapport coût-efficacité.

Direct link to Lay Summary Last update: 23.12.2020

Lay Summary (English)

Lead
SARS-CoV-2 is responsible for causing upper respiratory disease and pneumonia, threatening countless lives worldwide. SARS-CoV-2 critically relies on the reprogramming of cellular metabolism. We aim to identify vulnerabilities of the virus during its usurpation of the host cell and to use this knowledge to attenuate SARS-CoV-2.
Lay summary

Background

SARS-CoV-2, like all viruses, is dependent on hijacking the host cell translational machinery to achieve successful infection. It is important therefore to identify critical mechanisms that the virus uses to modify and reprogram cellular translation. Based on this knowledge, it will be possible to recode the SARS-CoV-2 genome and develop attenuated viruses for vaccine development. By combining this with established recoding strategies for virus attenuation, we will evaluate the attenuated viruses in cell culture and advanced animal models for different aspects of COVID-19.

Research aims

We will study SARS-CoV-2 RNA modifications and characterise the translational landscape and levels of cellular tRNA and tRNA modifications during infection in order to generate live-attenuated SARS-CoV-2 vaccine strains. This involves the generation of rationally re-coded SARS-CoV-2 and the assessment of attenuation, safety, and immunogenicity in several animal models.

Expected results and envisaged products

Our project is based on an iterative optimisation process. First, we generate vaccine strains instructed by molecular virus-host interactions in the context of RNA modification and translation. Second, we assess vaccine strain attenuation, pathogenicity and immunogenicity, and third, we refine the re-coded SARS-CoV-2 vaccine strains to optimally adjust virus attenuation to induce protective immune responses. The envisaged products are well characterised SARS-CoV-2 vaccine candidates that are rationally designed and assessed in vivo concerning attenuation, safety, and immunogenicity.

Specific contribution to tackle the current pandemic

Our project will contribute to the global effort in providing SARS-CoV-2 vaccines. We expect that first-generation of RNA-, subunit-, and vector-based vaccines will be swiftly available. However, we also expect that the resulting efficacy and safety data may reveal limitations of the first-generation vaccines. We predict that there will be a continued need to develop and distribute second-generation SARS-CoV-2 vaccines that overcome possible shortcomings of first-generation vaccines as regards, for example, ease of production, storage and cost-efficiency.

Direct link to Lay Summary Last update: 23.12.2020

Responsible applicant and co-applicants

Employees

Publications

Publication
Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding
Trimpert Jakob, Dietert Kristina, Firsching Theresa C., Ebert Nadine, Thi Nhu Thao Tran, Vladimirova Daria, Kaufer Susanne, Labroussaa Fabien, Abdelgawad Azza, Conradie Andelé, Höfler Thomas, Adler Julia M., Bertzbach Luca D., Jores Joerg, Gruber Achim D., Thiel Volker, Osterrieder Nikolaus, Kunec Dusan (2021), Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding, in Cell Reports, 36(5), 109493-109493.

Associated projects

Number Title Start Funding scheme
173085 Host innate immune responses to viral RNA 01.09.2017 Project funding
196387 A multidisciplinary approach to identify vulnerabilities of SARS-CoV-2 for vaccine development 01.06.2020 Special Call on Coronaviruses

Abstract

The newly discovered coronavirus (CoV) SARS-CoV-2 is responsible for the recent pandemic of upper respiratory disease and pneumonia that threatens countless lives across the globe. Like all viruses it critically relies on reprogramming of the cellular metabolism, in particular on hijacking the translation machinery of its host. The goal of this proposal is to identify vulnerabilities of the virus during its usurpation of the host cell. Specifically, we will comprehensively test multiple aspects that SARS-CoV-2 may use to hijack host translation. We will use this knowledge to rationally design re-coded coronavirus genomes in order to develop novel live-attenuated coronavirus vaccines. This strategy will not only be applicable for this virus but also for newly emerging zoonotic viruses in the future.Therefore, we will first ask whether the virus hijacks the host RNA modifications machinery to modify its own RNA genome to avoid detection by the host cell’s innate immune defense systems. Second, we will identify the host RNA modification machinery that mediates the modification of the viral genome. Third, we will examine whether viral RNA modifications facilitate the recruitment of the host translation machinery. To this end, we will use ribosome profiling and RNAseq in a high-resolution infection time course to quantitatively determine the translational response of the host cell. This will reveal how SARS-CoV-2 exploits the mRNA translation machinery of the host during its life cycle. Fourth, we will test whether the virus modulates the levels of tRNA and tRNA modifications to achieve efficient translation despite the diverging codon usage between its genome and the one of its host. Fifth, we will apply the knowledge gained to develop a series of synthetic attenuated viruses lacking, for example, RNA modifications or containing sequence elements that are difficult to translate during an infection. We will analyze the generated virus constructs both in vitro and in vivo and test selected viruses by ribosome profiling and in animal models. By combining these approaches, we will identify how SARS-CoV-2 interacts with its host and in particular its translation and RNA modification machineries. This will identify attenuated virus variants as well as drug targets and strategies to rationally design attenuated viruses that can be used for vaccine development also for other viruses.This proposal assembles an interdisciplinary team by joining the forces of five labs that combine expertise in diverse areas including molecular virology of coronaviruses, translation mechanisms (including that of viral RNAs), RNA modifications, codon pair deoptimization strategies, high-throughput sequencing, and different animal models for pathogenicity, transmission and immunogenicity. Importantly, our multi-faceted approach will allow us to go beyond the current state of the art, in particular since this team has direct access to live virus samples, various animal models, BSL3 laboratories and animal facilities, and the ability to create recombinant SARS-CoV-2 for experimentation. We are confident that the combined knowledge generated on this new virus can rapidly facilitate vaccine development.Importantly, we will make our initial ribosome profiling and RNA methylation data available immediately after acquisition to speed up research during this ongoing crisis.
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